Way back in Summer Knight when Ebenezar was introducing Harry to Martha Liberty and LtW to ask for their support in the vote, didn't Martha say something to Eb along the lines of "You know what he was meant to be"?
That reminds me there was one thing I left out of my summary about what we know and don't know and Justin. It's something will all know, but I think it's easy to forget; Justin was Simon Pietrovich's apprentice. Those readers who think Justin is still alive see him as the likely culprit who told the Red Court how to disable or defeat Simon's wards. Of course, because Harry had been Justin's apprentice it was suggested by Senior Council member LaFortier that Harry was the guilty party.
However, to get to your post, I don't think we know what Martha Liberty meant by that statement. I don't think she meant that Harry was meant to be Justin's enforcer. The fact that Harry rebelled against Justin would seem to weigh against that interpretation. Also, even in a worse case scenario, if Harry had gone bad at a young age, how is one more Warlock a danger to the White Council? The Council must have been afraid that Harry was something special, but in a very bad way.
One more thing to consider. If the White Council learned that Harry is starborn, we don't know whether that is a good thing or a bad thing from the Council's perspective. Past starborn individuals may have catalysts for great destruction or seen as enemies of the Council, or at least enemies of the established order. I keep thinking about Mother Winter referring to Harry as a weapon, in Cold Days. Maybe the Senior Council saw Harry that way too, only they thought he was a major weapon that could be pointed at them, not just at Outsiders. Now that I think about it, the Senior Council might not even know Harry; or any starborn individual, can wield power over Outsiders. Just because Lash and Margaret LeFey knew this, it doesn't mean it's general knowledge in the magical world.